@nux--Yukari Sakamoto is your friend? Cool. She's always been very helpful and knowledgeable. Seems like she'd be fun to eat with!
I've not been to Creations de Narisawa. I was curious about it, but some very reliable Chow members nixed it. It's mostly furreners in Japan for short visits who rave about it, I was told.
For Tokyo, are you considering Tokyo-posts of French restaurants? I had an excellent meal at Michel Troisgrois, but I know you go to France relatively frequently, so it might not be something in which you're interested.
Is Tapas Molecular Bar on your list? It was kind of fun, but I didn't think the food was memorable at all.
In Kyoto, Ten-you is still my favourite tempura place (in the article to which nux linked, it's transliterated as Ten'yu, but on restaurant's business cards and other literature, it's Ten-you). It's just so typically Kyoto, and I much preferred it to Tempura Kondo in Tokyo. It's owned by the Tawaraya folks (of the famous ryokan).
I'd love for you to visit O-men, too. I've always wondered if the NYC branch was much different from the Kyoto branches (I've only been to the one off Shijo--not the one in Gion, but the one closer to Teramachi or thereabouts). Famous for their udon, but I like their other stuff better (I'm not a big fan of udon, though).
Also, Okariba in Kyoto. I never got to go there, but I recommended it to Peter Green (eG) and he enjoyed it. Basashi, wild boar, crickets, bees. . . what more could you want? You can find his post about it here http://egullet.org/p1555036
and the bento.com listing is here http://www.bento.com...ai/search4k.php
. Certainly not a posh place, though.